The attackers also daubed slogans in blue paint including "Shit Jews" and the Nazi rallying cry "Sieg Heil" on the exterior walls of the graveyard in the early hours of Monday morning.
"We are tracking one suspect in particular. There was probably a group with him but I cannot say for sure," a police spokeswoman told news agency AFP.
Last week, a rabbi was beaten in broad daylight on a Berlin street by four youths who also threatened to kill his young daughter. Police suspect the assailants were of Arab origin.
The attack, which sent shock waves through the country's 200,000-strong Jewish community and made international headlines, came amid a bitter debate over a recent court ruling declaring that religious circumcision as practiced by Jews and Muslims amounted to grievous bodily harm.
Last year, 30 Jewish gravestones were desecrated in the western city of Essen on the night of April 20, Adolf Hitler's birthday.
Three men aged 18 to 20 were arrested, according to a Berlin-based group fighting hate crimes, the Amadeu Antonio Foundation.